Structural basis for intermodular communication in assembly-line polyketide biosynthesis

Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs over the nearly four decades from 01/1981 to 09/2019. J. Nat. Prod. 83, 770–803 (2020).Article 
CAS 
PubMed 

Google Scholar 
Robertsen, H. L. & Musiol-Kroll, E. M. Actinomycete-derived polyketides as a source of antibiotics and lead structures for the development of new antimicrobial drugs. Antibiotics (Basel) 8, 157 (2019).Kirst, H. A. The spinosyn family of insecticides: realizing the potential of natural products research. J. Antibiot. (Tokyo) 63, 101–111 (2010).Article 
CAS 
PubMed 

Google Scholar 
Toopaang, W. et al. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat. Prod. Rep. 39, 2008–2029 (2022).Article 
CAS 
PubMed 

Google Scholar 
Nivina, A., Yuet, K. P., Hsu, J. & Khosla, C. Evolution and diversity of assembly-line polyketide synthases. Chem. Rev. 119, 12524–12547 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Klaus, M. & Grininger, M. Engineering strategies for rational polyketide synthase design. Nat. Prod. Rep. 35, 1070–1081 (2018).Article 
CAS 
PubMed 

Google Scholar 
Soohoo, A. M., Cogan, D. P., Brodsky, K. L. & Khosla, C. Structure and mechanisms of assembly-line polyketide synthases. Annu. Rev. Biochem. 3, 471–498 (2024).Article 

Google Scholar 
Dutta, S. et al. Structure of a modular polyketide synthase. Nature 510, 512–517 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Whicher, J. R. et al. Structural rearrangements of a polyketide synthase module during its catalytic cycle. Nature 510, 560–564 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Herbst, D. A. et al. The structural organization of substrate loading in iterative polyketide synthases. Nat. Chem. Biol. 14, 474–479 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wang, J. et al. Structural basis for the biosynthesis of lovastatin. Nat. Commun. 12, 867 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cogan, D. P. et al. Mapping the catalytic conformations of an assembly-line polyketide synthase module. Science 374, 729–734 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bagde, S. R., Mathews, I. I., Fromme, J. C. & Kim, C.-Y. Modular polyketide synthase contains two reaction chambers that operate asynchronously. Science 374, 723–729 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Grininger, M. Enzymology of assembly line synthesis by modular polyketide synthases. Nat. Chem. Biol. 19, 401–415 (2023).Article 
CAS 
PubMed 

Google Scholar 
Kao, C. M., Pieper, R., Cane, D. E. & Khosla, C. Evidence for two catalytically independent clusters of active sites in a functional modular polyketide synthase. Biochemistry 35, 12363–12368 (1996).Article 
CAS 
PubMed 

Google Scholar 
Witkowski, A. et al. Dibromopropanone cross-linking of the phosphopantetheine and active-site cysteine thiols of the animal fatty acid synthase can occur both inter- and intrasubunit. Reevaluation of the side-by-side, antiparallel subunit model. J. Biol. Chem. 274, 11557–11563 (1999).Article 
CAS 
PubMed 

Google Scholar 
Stoops, J. K. & Wakil, S. J. Yeast fatty acid synthetase: structure–function relationship and nature of the β-ketoacyl synthetase site. Proc. Natl Acad. Sci. USA 77, 4544–4548 (1980).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Miyazawa, T., Hirsch, M., Zhang, Z. & Keatinge-Clay, A. T. An in vitro platform for engineering and harnessing modular polyketide synthases. Nat. Commun. 11, 80 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gokhale, R. S., Tsuji, S. Y., Cane, D. E. & Khosla, C. Dissecting and exploiting intermodular communication in polyketide synthases. Science 284, 482–485 (1999).Article 
CAS 
PubMed 

Google Scholar 
Broadhurst, R. W., Nietlispach, D., Wheatcroft, M. P., Leadlay, P. F. & Weissman, K. J. The structure of docking domains in modular polyketide synthases. Chem. Biol. 10, 723–731 (2003).Article 
CAS 
PubMed 

Google Scholar 
Tsuji, S. Y., Cane, D. E. & Khosla, C. Selective protein−protein interactions direct channeling of intermediates between polyketide synthase modules. Biochemistry 40, 2326–2331 (2001).Article 
CAS 
PubMed 

Google Scholar 
Henderson, R. et al. Outcome of the first electron microscopy validation task force meeting. Structure 20, 205–214 (2012).Article 
CAS 
PubMed 

Google Scholar 
Kapur, S., Chen, A. Y., Cane, D. E. & Khosla, C. Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase. Proc. Natl Acad. Sci. USA 107, 22066–22071 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kapur, S. et al. Reprogramming a module of the 6-deoxyerythronolide B synthase for iterative chain elongation. Proc. Natl Acad. Sci. USA 109, 4110–4115 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Charkoudian, L. K. et al. Probing the interactions of an acyl carrier protein domain from the 6-deoxyerythronolide B synthase. Protein Sci. 20, 1244–1255 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Squire, C. M., Goss, R. J. M., Hong, H., Leadlay, P. F. & Staunton, J. Catalytically active tetramodular 6-deoxyerythonolide B synthase fusion proteins. ChemBioChem 4, 1225–1228 (2003).Article 
CAS 
PubMed 

Google Scholar 
Cogan, D. P. et al. Antibody probes of module 1 of the 6-deoxyerythronolide B synthase reveal an extended conformation during ketoreduction. J. Am. Chem. Soc. 142, 14933–14939 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhao, Y., Schmid, M. F., Frydman, J. & Chiu, W. CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Nat. Commun. 12, 4754 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tsai, S. C. et al. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc. Natl Acad. Sci. USA 98, 14808–14813 (2001).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Klaus, M. et al. Protein–protein interactions, not substrate recognition, dominate the turnover of chimeric assembly line polyketide. J. Biol. Chem. 291, 16404–16415 (2016).Whicher, J. R. et al. Cyanobacterial polyketide synthase docking domains: a tool for engineering natural product biosynthesis. Chem. Biol. 20, 1340–1351 (2013).Article 
CAS 
PubMed 

Google Scholar 
Zhang, L. et al. Characterization of giant modular PKSs provides insight into genetic mechanism for structural diversification of aminopolyol polyketides. Angew. Chem. Int. Ed. Engl. 56, 1740–1745 (2017).Article 
CAS 
PubMed 

Google Scholar 
Keatinge-Clay, A. T. Polyketide synthase modules redefined. Angew. Chem. Int. Ed. Engl. 56, 4658–4660 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sugimoto, Y. et al. Freedom and constraint in engineered noncolinear polyketide assembly lines. Chem. Biol. 22, 229–240 (2015).Article 
CAS 
PubMed 

Google Scholar 
Mabesoone, M. F. J. et al. Evolution-guided engineering of trans-acyltransferase polyketide synthases. Science 383, 1312–1317 (2024).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lowry, B., Li, X., Robbins, T., Cane, D. E. & Khosla, C. A turnstile mechanism for the controlled growth of biosynthetic intermediates on assembly line polyketide synthases. ACS Cent. Sci. 2, 14–20 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kim, C.-Y. et al. Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase. Biochemistry 43, 13892–13898 (2004).Article 
CAS 
PubMed 

Google Scholar 
Li, X. et al. Structure–function analysis of the extended conformation of a polyketide synthase module. J. Am. Chem. Soc. 140, 6518–6521 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).Article 
CAS 
PubMed 

Google Scholar 
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).Article 
CAS 
PubMed 

Google Scholar 
Asarnow, D., Palovcak, E. & Cheng, Y. asarnow/pyem: UCSF pyem v0.5. Zenodo https://doi.org/10.5281/zenodo.3576630 (2019).Meng, E. C. et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32, e4792 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Adams, P. D. et al. The Phenix software for automated determination of macromolecular structures. Methods 55, 94–106 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, gky427 (2018).Article 

Google Scholar 
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar